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RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins
(Nucleic acids research, 2013)
RBPmotif web server (http://www.rnamotif.org) implements tools to identify binding preferences of RNA-binding proteins (RBPs). Given a set of sequences that are known to be bound and unbound by the RBP of interest, RBPmotif ...
MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules
(Bioinformatics, 2019)
Motivation: Genomic analyses from large cancer cohorts have revealed the mutational heterogeneity problem
which hinders the identification of driver genes based only on mutation profiles. One way to tackle this problem ...
JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis
(Bioinformatics, 2015)
Motivation: Rapid advances in genotyping and genome-wide association studies have enabled the discovery of many new genotype–phenotype associations at the resolution of individual markers. However, these associations explain ...
Target-independent prediction of drug synergies using only drug lipophilicity
(Journal of Chemical Information and Modeling, 2014)
Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency ...
Modeling gene regulation in liver hepatocellular carcinoma with random forests
(BioMed Research International, 2016)
Liver hepatocellular carcinoma (HCC) remains a leading cause of cancer-related death. Poor understanding of the mechanisms underlying HCC prevents early detection and leads to high mortality. We developed a random forest ...
A translational repression complex in developing mammalian neural stem cells that regulates neuronal specification
(Neuron, 2018)
The mechanisms instructing genesis of neuronal sub-types from mammalian neural precursors are not well understood. To address this issue, we have characterized the transcriptional landscape of radial glial precursors (RPs) ...
Chemogenomics and orthology‐based design of antibiotic combination therapies
(Molecular Systems Biology, 2016)
Combination antibiotic therapies are being increasingly used in
the clinic to enhance potency and counter drug resistance.
However, the large search space of candidate drugs and dosage
regimes makes the identification ...
MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules
(Bioinformatics, 2019)
Motivation: Genomic analyses from large cancer cohorts have revealed the mutational heterogeneity problem which hinders the identification of driver genes based only on mutation profiles. One way to tackle this problem is ...
Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation
(Nucleic Acids Research, 2016)
Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research to date has ...
Predicting clinical outcomes in neuroblastoma with genomic data integration
(Biology Direct, 2018)
Background: Neuroblastoma is a heterogeneous disease with diverse clinical outcomes. Current risk group models require improvement as patients within the same risk group can still show variable prognosis. Recently collected ...
